DNA-functionalized particles have great potential for the design of complexself-assembled materials. The major hurdle in realizing crystal structures fromDNA-functionalized particles is expected to be kinetic barriers that trap thesystem in metastable amorphous states. Therefore, it is vital to explore themolecular details of particle assembly processes in order to understand theunderlying mechanisms. Molecular simulations based on coarse-grained models canprovide a convenient route to explore these details. Most of the currentlyavailable coarse-grained models of DNA-functionalized particles ignore keychemical and structural details of DNA behavior. These models therefore arelimited in scope for studying experimental phenomena. In this paper, we presenta new coarse-grained model of DNA-functionalized particles which incorporatessome of the desired features of DNA behavior. The coarse-grained DNA model usedhere provides explicit DNA representation (at the nucleotide level) andcomplementary interactions between Watson-Crick base pairs, which lead to theformation of single-stranded hairpin and double-stranded DNA. Aggregationbetween multiple complementary strands is also prevented in our model. We studyinteractions between two DNA- functionalized particles as a function of DNAgrafting density, lengths of the hybridizing and non-hybridizing parts of DNA,and temperature. The calculated free energies as a function of pair distancebetween particles qualitatively resemble experimental measurements ofDNA-mediated pair interactions.
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